All i can suggest is read the warranty the company offers before making this kind of investment, this way you know what they have to offer if there is an issue. If you don't like the terms then look at the next brand are just stay stock. I don't right the rules man I'm just a tester for them.
The question was asked and i simply gave my opinion of what some of the known issues with this tranny were.
At the end of the day the transmission company has done its job to build a tranny that is capable of holding X amount of power. Its not their problem if tuning jacks them up, although they usually warranty them anyway.
My best advise is to make sure you use a reputable tuner that has many happy customers. Proper tuning is the life of the 68rfe!!!
Towing is not an issue with the Mega! What has been your issue on the ones you've had?